Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region

A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.


General Remarks:
This is an interesting and well written manuscript.The title is appropriate for the content of this article.The abstract is concise and accurately summarizes the essential information of the paper.The introduction provides an excellent, generalized background of the topic and this gives the reader an appreciation of the wide range of applications to the technology (nucleic acid extraction and shotgun sequencing) used for this research.The authors collected a unique dataset and the data were analyzed following laid down scientific methodology.The experimental design is standard and appropriate for this study.The authors provided adequate information especially in the materials and methods to make this research experiment capable of been reproduced by a capable research scientist.
The main strength of this paper is that it addresses an interesting topic and it contributes to our understanding on the importance of soil resistome studies and the associated antibiotic resistance genes (ARG) dissemination mechanisms.The manuscript also finds a novel solution based on a carefully selected set of rules and procedures and finally provides a clear solution to the research questions asked.Literature cited in the manuscript, are relevant for this study.The figures and tables are well organized, easy to interpret and follows a systematic and a logical order.It improves our understanding of the importance of the spatial variability of soil resistomes and how ARG depends on microbial community structure as well as its functional potential.
Generally, the study is of great significance and contributes extensively to our understanding of soil microbial communities to soil agrobiochemical cycles is critical for predicting terrestrial ecosystem feedbacks in the study area.I recommend this manuscript (PONE-D-23-21640) for publication after some corrections have been taken into account.Thus, to make the manuscript more reader friendly to an international audience, I suggest that the authors, if possible, should rephrase the title of the manuscript, some sentences in the manuscript and also include the significant level (e.g., 0.05, 0.01, 0.001) and the p -values (e.g., p < 0.03), if possible, into their findings where significant or not significant and/or where positive or negative corelation (r = 0.00; p -value) is reported in the manuscript.

Specific Remarks:
Pg. 3 Line 83 -84: Metabolites produced by the rhizobiome are important contributors to the quality, fragrance and distinctive personality of the products (5,6).

Pg. 4
Line 86 -88: The adaptation abilities of the microbiota depend on community plasticity.Network analysis-based approaches can help in better understanding the intricate nature of microbemicrobe and microbe-community interactions.
Please rephrase the above sentence as: The adaptation abilities of the microbiota depend on community plasticity.Network analysis-based approaches can help understand the intricate nature of microbe-microbe and microbe-community interactions.

Pg. 10
Line 244 -245: At the phylum level, 90.0% of the Bacteria and 70.0% of the Fungi OTUs were present in our sample population.
Please edit as: "At the phylum level, 70% and 90% of Fungi OTUs and Bacteria were present in our sample population, respectively".

Pg. 11
Line 255 -256: Comprehensive comparisons of the soil samples of the Tokaj-Mád vineyards were made based on the hierarchical clustering of the bacterial and fungal 100% core microbiota (Fig. 5).

Figures and Tables
Dear authors, please increase the resolution of the figures and tables.For example, Figures 2A,and 2B,Figures 7A,and 7B,Figures 9D,and Figures and TablesDear authors, please increase the resolution of the figures and tables.For example, Figures2A,  and 2B, Figures 7A, and 7B, Figures 9D, and 9F.